To me, they both sound okay. "A" sounds to me like she hadn't planned to have her son, and she still wishes she hadn't had him, while "B" sounds to me like she hadn't planned to have her son, but she doesn't consider him an "accident" anymore. The reason they sound that way to me is that they could be rewritten with quotations, and in my opinion they'd be rewritten as: A. She told her son, "You are an accident--I wasn't planning to have a child." B. She told her son, "You were an accident--I wasn't planning to have a child."

Letter A is correct. You would not use the past perfect tense to describe his birth in this particular example.